The presence of Alicyclobacillus acidoterrestris in stored juices can be difficult to detect. In this study the effects of storage temperature, headspace and agitation of juice containers was investigated. The results indicate that the amount of headspace has a significant effect on growth of vegetative cells and spores of A. acidoterrestris at 35 °C. Intermittent shaking before sampling increased growth and therefore probable detection rates at 30 °C, Agitating containers and sampling from several areas within containers is therefore recommended for determining whether A. acidoterrestris is present or absent from stored juice, especially in large containers.